Continuity mistake: The sequence in which Dragon is chasing Mrs. Brisby through the field, up the tree and eventually into the mill's lake, watch his eyes. The original placement is (from viewer's perspective) blue on the right and gold on the left. When he chases her up the tree the gold one is visible on the right, it then switches back when the camera cuts back to a wide shot. This happens again a few seconds later near the lake.

Continuity mistake: At one point during "Flying Dreams" when Timothy is being cared for by Mrs. Brisby and the other children gather at his bedside, his left arm appears in various positions as the shots change - instantly on top of and then beneath the quilt.

Continuity mistake: While Mrs. Fitzgibbons is in the bedroom talking to her husband about NIMH, she pulls a window shade all the way down. But from the next view, where several rats are transporting an extension cord across the front yard's walkway, the shade is back to its original position again - about halfway up.